The technique that’s revolutionizing aquatic science

Looking for brook trout? Try environmental DNA.

Back in 2009, I passed a memorable summer in Yellowstone, helping the National Park Service exterminate the alien trout that past generations of biologists and anglers, in their finite wisdom, had carelessly introduced. One week, in an effort to purge the park’s northeast corner of invasive brook trout, we used backpack shockers: ungainly apparatuses that zapped streams with electric current, stunning nearby fish into submission so that we could net and kill the interloping brookies.

It was hard work, plagued by uncertainty and inefficiency. We once waded up a steep tributary for hours, fruitlessly waving our electrodes beneath logjams and waterfalls, certain that the stream was uncontaminated — only to shock an intrepid, lonely brook trout at the headwaters. Our sweat-soaked shoulders slumped. A day of back-breaking work to find a single fish? There had to be a better way.

The author holds up a non-native brook trout, plucked from a lake in Yellowstone National Park. Photo by Elise Rose.

Now, I’m happy to report, such a way exists: environmental DNA, or eDNA. The scientific technique allows researchers to sample water or soil for minute traces of animal DNA — morsels of shed skin, fecal matter or reproductive material — to verify the presence of their target critter. Have brook trout or other invasives infiltrated a watershed? Is the cryptic Idaho giant salamander hiding in a mountain creek? Just grab a few water samples and run some polymerase chain reactions (PCRs) — a method for amplifying DNA that’s used in everything from forensics to diagnosing hereditary disease — and voila, you’ve got your answer. During my time in Yellowstone, eDNA could have saved us hours, even days, of arduous searching.

No wonder, then, that scientists around the West are spreading the eDNA gospel. Among the converts is Matthew Laramie, a U.S. Geological Survey ecologist who recently employed the technique to find summer chinook salmon in northern Washington's Methow and Okanagan basins. The fish head upriver in spring, when melt-swollen creeks make traditional sampling methods like snorkeling or electrofishing impractical. By contrast, says Laramie, using eDNA barely requires getting out of the car: “A single person could sample the whole Okanagan Basin in a day or two.”

More important than convenience, of course, is accuracy. Fortunately, eDNA passes that test. In streams where Laramie knew chinook were present, he generally found their DNA; in streams that the fish couldn’t access, he didn’t. Now that the test has been proven effective on chinook, says Laramie, it can be used to track the salmon restoration efforts of the Colville Confederated Tribes, which plan to reintroduce spring chinook into the Okanagan within the year.

eDNA is also being employed to combat those pesky brook trout, an eastern species that have displaced bull trout, a threatened native cousin, in many Western streams. Tracking the fishes’ relative distributions may help researchers like Taylor Wilcox, a PhD student at the University of Montana, understand exactly what happens when the invader enters a system — especially whether bull trout can survive by fleeing to connected streams elsewhere in the watershed. Such a vast study is tailor-made for environmental DNA. “With eDNA, you can have really high detection probability over very large scales, and the cost of sampling is lower than doing backpack electrofishing,” Wilcox says. Indeed, he and collaborators have picked up traces of brook trout genetic material in situations where backpack electroshocking had stunned nary a fish.

Still, eDNA remains immature in many ways. The technique has only been in widespread use for a few years, and there are important questions it can’t yet reliably answer. How many fish — or frogs, or salamanders — live in a stream? Are they old or young, healthy or sick? Though traces of Asian carp DNA have led some scientists to suspect that the infamous invader has finally reached the Great Lakes, others claim the samples could have come from bird droppings or boats. Distinguishing the DNA of close relatives like brook and bull trout, or coho and chinook salmon, is also challenging. Scooping up water samples might be easy, but creating sufficiently sensitive PCR assays, claims Laramie, "is where the hard work of this method comes in."

Nonetheless, eDNA is already changing the face of aquatic science and conservation — and as methods improve, its role will only expand. “There are still so many unknowns,” Laramie says with relish. “It’s a field that’s just ripe for research.”

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